The 3D-Interologs is a cross-species interacting database inferring from three-dimensional (3D) protein structure complexes and a novel scoring function by using 3D-domain interologs. For a query protein, the 3D-Interologs database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the novel scoring function and structure complexes, 3D-Interologs provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species is able to use to study on protein-protein evolution, protein functions, and cross-referencing of proteins.

Figure 1 shows the overview of our method using 3D-domain interologs to extract domain annotated protein-protein interactions from 3D protein complexes by performing the following steps: (i) identifying the interactive domains (domains a and b) and contact residues of a 3D complex (containing chains A and B) in the PDB; (ii) identifying the interactive domains in the complex using the domain boundary defined by the SCOP database; (iii) searching two protein families (A' and B') which contain the corresponding domains (a and b) from the Swiss-Prot database; (iv) evaluating evaluate how well the interfaces of protein pair (A' and B').
Figure 1. Overview of our method using 3D-domain interologs.